ricalessandri / misctab

Scripts for binary mixtures

Setup and Run Binary Mixtures with Martini

You need the following (1 script and 1 folder):

 run_misctab_GMX16_cartes.sh
 template-miscibility/

Submit a new mixture with:

 ./run_misctab_GMX16_cartes.sh  BENZ  3  CHEX  2  293.15

where the arguments correspond to: 1) "BENZ" -> label of molecule_A; 2) "3" -> no. of beads of molecule_A; 3) "CHEX" -> label of molecule_B; 4) "2" -> no. of beads of molecule_B; 5) 293.15 -> temperature.

Note that the script uses a existing starting box named as:

 3bead2bead-80008000.gro

if available or creates one from scratch; the name contains the no. of beads per molecule (3 beads for molecule_A, 2 beads for molecule_B) and the no. of molecules per molecules (8000 for molecule_A, 8000 for molecule_B). You can add yourself new pre-equilibrated starting boxes following the syntax above to the folder "template-miscibility/".

To adapt the script to run somewhere else than Cartesius:

1. Potentially need to modify the "sbatch" line in ./run_misctab_GMX16_cartes.sh
2. Check the header of template-miscibility/setup_and_run_mixture.sh which contains SBATCH commands such as: #SBATCH --partition=short and command aliases such as: MDRUN="srun gmx_mpi mdrun".